The 'Ferret' analytical engine, developed originally by the Y-12 National Security complex of the U.S. Department of Energy to seek classified data and associations in documents and present its findings in the light of formal rules, requires a structured information base that represents not just individual facts but a set of implications and a collection of rules. The fundamental knowledge base is evolving towards forms that enhance flexibility and portability. The developers early realized that the knowledge base can be captured in XML by a series of trees that represent taxonomies, analytical structures, and specific indicative facts, but over this a topic map is needed to express links across the trees. Above this, the classification rules could form another topic map that points into the lower layers. In its latest form, however, the knowledge base has come to entirely represented in a topic map.